A combination of gene expression ranking and co-expression network analysis increases discovery rate in large-scale mutant screens for novelArabidopsis thalianaabiotic stress genes

Machine Learning-Based Differential Network Analysis: A Study of Stress-Responsive Transcriptomes in Arabidopsis

(2014) C. Ma et al.   PLANT CELL

Systematic Identification of Cell-Wall Related Genes in Populus Based on Analysis of Functional Modules in Co-Expression Network

(2014) Bin Cai et al.   PLoS One

Roles of CAMTA transcription factors and salicylic acid in configuring the low-temperature transcriptome and freezing tolerance of Arabidopsis

(2013) YongSig Kim et al.   PLANT JOURNAL

A Computational Systems Biology Study for Understanding Salt Tolerance Mechanism in Rice

(2013) Juexin Wang et al.   PLoS One

Towards revealing the functions of all genes in plants

(2013) Seung Yon Rhee et al.   TRENDS IN PLANT SCIENCE

The MORPH Algorithm: Ranking Candidate Genes for Membership in Arabidopsis and Tomato Pathways

(2012) O. Tzfadia et al.   PLANT CELL

Gene-Sharing Networks Reveal Organizing Principles of Transcriptomes inArabidopsisand Other Multicellular Organisms

(2012) Song Li et al.   PLANT CELL

Systems Analysis of Plant Functional, Transcriptional, Physical Interaction, and Metabolic Networks

(2012) George W. Bassel et al.   PLANT CELL

Unique Drought Resistance Functions of the Highly ABA-Induced Clade A Protein Phosphatase 2Cs

(2012) G. B. Bhaskara et al.   PLANT PHYSIOLOGY

Systematic Identification of Functional Plant Modules through the Integration of Complementary Data Sources

(2012) K. S. Heyndrickx et al.   PLANT PHYSIOLOGY

Reverse Engineering: A Key Component of Systems Biology to Unravel Global Abiotic Stress Cross-Talk

(2012) Swetlana Friedel et al.   Frontiers in Plant Science

NAC transcription factors in plant abiotic stress responses

(2011) Kazuo Nakashima et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

Interaction of Arabidopsis DET1 with CCA1 and LHY in Mediating Transcriptional Repression in the Plant Circadian Clock

(2011) On Sun Lau et al.   MOLECULAR CELL

Abscisic Acid Signal off the STARTing Block

(2011) Archana Joshi-Saha et al.   Molecular Plant

Functional Network Construction inArabidopsisUsing Rule-Based Machine Learning on Large-Scale Data Sets

(2011) George W. Bassel et al.   PLANT CELL

A Large-Scale Genetic Screen in Arabidopsis to Identify Genes Involved in Pollen Exine Production

(2011) A. A. Dobritsa et al.   PLANT PHYSIOLOGY

Chloroplast 2010: A Database for Large-Scale Phenotypic Screening of Arabidopsis Mutants

(2011) Y. Lu et al.   PLANT PHYSIOLOGY

The Impact of Multifunctional Genes on "Guilt by Association" Analysis

(2011) Jesse Gillis et al.   PLoS One

Genome-wide network model capturing seed germination reveals coordinated regulation of plant cellular phase transitions

(2011) G. W. Bassel et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genetic dissection of the biotic stress response using a genome-scale gene network for rice

(2011) I. Lee et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A general co-expression network-based approach to gene expression analysis: comparison and applications

(2010) Jianhua Ruan et al.   BMC Systems Biology

Reverse Genetic Screening Identifies Five E-class PPR Proteins Involved in RNA Editing in Mitochondria ofArabidopsis thaliana

(2010) Mizuki Takenaka et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Assessment of effectiveness of the network-guided genetic screen

(2010) Eiru Kim et al.   Molecular BioSystems

Overexpression of the ethylene-responsive factor gene BrERF4 from Brassica rapa increases tolerance to salt and drought in Arabidopsis plants

(2010) Yean Joo Seo et al.   MOLECULES AND CELLS

Rational association of genes with traits using a genome-scale gene network for Arabidopsis thaliana

(2010) Insuk Lee et al.   NATURE BIOTECHNOLOGY

Expander: from expression microarrays to networks and functions

(2010) Igor Ulitsky et al.   Nature Protocols

RD20, a Stress-Inducible Caleosin, Participates in Stomatal Control, Transpiration and Drought Tolerance in Arabidopsis thaliana

(2010) Yann Aubert et al.   PLANT AND CELL PHYSIOLOGY

Evolutionary and comparative analysis of MYB and bHLH plant transcription factors

(2010) Antje Feller et al.   PLANT JOURNAL

Coexpression Analysis Identifies Rice Starch Regulator1, a Rice AP2/EREBP Family Transcription Factor, as a Novel Rice Starch Biosynthesis Regulator

(2010) F.-F. Fu et al.   PLANT PHYSIOLOGY

The Association of Multiple Interacting Genes with Specific Phenotypes in Rice Using Gene Coexpression Networks

(2010) Stephen P. Ficklin et al.   PLANT PHYSIOLOGY

Arabidopsis gene co-expression network and its functional modules

(2009) Linyong Mao et al.   BMC BIOINFORMATICS

Co-expression tools for plant biology: opportunities for hypothesis generation and caveats

(2009) BJ��RN USADEL et al.   PLANT CELL AND ENVIRONMENT

Assembly of an Interactive Correlation Network for the Arabidopsis Genome Using a Novel Heuristic Clustering Algorithm

(2009) M. Mutwil et al.   PLANT PHYSIOLOGY

Functional-genomics-based identification of genes that regulate Arabidopsis responses to multiple abiotic stresses

(2008) PRAGYA KANT et al.   PLANT CELL AND ENVIRONMENT

An Abscisic Acid-Induced Protein, HVA22, Inhibits Gibberellin-Mediated Programmed Cell Death in Cereal Aleurone Cells

(2008) W.-J. Guo et al.   PLANT PHYSIOLOGY

Systems approach identifies an organic nitrogen-responsive gene network that is regulated by the master clock control gene CCA1

(2008) R. A. Gutierrez et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mutations in AtPS1 (Arabidopsis thaliana Parallel Spindle 1) Lead to the Production of Diploid Pollen Grains

(2008) Isabelle d'Erfurth et al.   PLoS Genetics

The Clock Protein CCA1 and the bZIP Transcription Factor HY5 Physically Interact to Regulate Gene Expression in Arabidopsis

(2007) Christos Andronis et al.   Molecular Plant